I've seen this problem on Win95/98/ME systems when running LabVIEW applications with continuous serial I/O. It was a Windows related problem.
When you restart the computer, does the clock revert to the correct time? If so that's not a MB clock/battery problem. That's Windows time routines that are slowed down. The time is synched with RTC on startup only.
If I remember correctly, the problem is related to Power Saving modes in the BIOS and can be corrected changing the settings.
Search microsoft.com for more information.